Set up
suppressPackageStartupMessages({
library(tidyverse)
})
Read in data and process
pbta_df <- readr::read_tsv(pbta_file, guess_max = 100000, show_col_types = FALSE) %>%
select(Kids_First_Participant_ID, Kids_First_Biospecimen_ID, cg_multiple, cg_id, cgGFAC, tumor_descriptor)
genomic_paired_df <- readr::read_tsv(genomic_paired_file, guess_max = 100000, show_col_types = FALSE) %>%
left_join(pbta_df, by = c("Kids_First_Participant_ID"))
descriptors_df <- genomic_paired_df %>%
group_by(Kids_First_Participant_ID) %>%
summarize(descriptors = paste(sort(tumor_descriptor), collapse = ", "),)
# Vector to order timepoints
timepoints <- c("Diagnosis", "Progressive", "Recurrence", "Deceased", "Second Malignancy", "Unavailable")
# Create df to use for plots
df_plot <- genomic_paired_df %>%
left_join(descriptors_df, by = c("Kids_First_Participant_ID", "descriptors")) %>%
mutate(td_cgGFAC = case_when(grepl("Deceased", tumor_descriptor) ~ "xDeceased",
TRUE ~ tumor_descriptor),
log10_tmb = abs(log10(tmb)),
cg_id_kids = paste(cg_id, Kids_First_Participant_ID, sep = "_"),
cg_id_kids = str_replace(cg_id_kids, "/", "_"),
cg_id_kids = str_replace(cg_id_kids, "-", "_"),
cg_id_kids = str_replace_all(cg_id_kids, " ", "_"),
tumor_descriptor = factor(tumor_descriptor),
tumor_descriptor = fct_relevel(tumor_descriptor, timepoints))
# Let's count number of samples
count_df <- df_plot %>%
group_by(tumor_descriptor, cg_id, Kids_First_Biospecimen_ID, Variant_Classification) %>%
dplyr::count(cg_id)
Define parameters for plots
# Read color palette
palette_df <- readr::read_tsv(palette_file, guess_max = 100000, show_col_types = FALSE)
# Define and order palette
palette <- palette_df$hex_codes
names(palette) <- palette_df$color_names
Alterations per timepoint
# Define parameters for function
x_value <- count_df$tumor_descriptor
title <- paste("Variant types in PBTA cohort", sep = " ")
# Run function
fname <- paste0(plots_dir, "/", "Alteration_type_timepoints_barplots.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_timepoints_barplots.pdf"
p <- create_stacked_barplot_variant(count_df = count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 6, height = 6)
print(p)
dev.off()
quartz_off_screen
2

Alterations per timepoint in each cancer type
cg_id_id <- as.character(unique(count_df$cg_id))
cg_id_id <- sort(cg_id_id, decreasing = FALSE)
cg_id_id
[1] "Adamantinomatous Craniopharyngioma" "Atypical Teratoid Rhabdoid Tumor"
[3] "Chordoma" "Choroid plexus carcinoma"
[5] "CNS Embryonal tumor" "Craniopharyngioma"
[7] "Diffuse midline glioma" "Dysembryoplastic neuroepithelial tumor"
[9] "Embryonal tumor with multilayer rosettes" "Ependymoma"
[11] "Ewing sarcoma" "Ganglioglioma"
[13] "Glial-neuronal tumor" "Hemangioblastoma"
[15] "High-grade glioma" "Low-grade glioma"
[17] "Malignant peripheral nerve sheath tumor" "Medulloblastoma"
[19] "Meningioma" "Neuroblastoma"
[21] "Neurofibroma/Plexiform" "Pilocytic astrocytoma"
[23] "Rosai-Dorfman disease" "Schwannoma"
# Define parameters for function
x_value <- count_df$Kids_First_Biospecimen_ID
title <- paste("Variant types in PBTA cohort across cancer groups", sep = " ")
# Run function
fname <- paste0(plots_dir, "/", "Alteration_type_timepoints_cg_id_barplots.pdf")
print(fname)
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/Alteration_type_timepoints_cg_id_barplots.pdf"
p <- create_stacked_barplot_variant_cg_id(count_df = count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 30, height = 18)
print(p)
dev.off()
quartz_off_screen
2

Alterations per timepoint in each cancer type defined by cgGFAC
df_plot_cgGFAC <- df_plot %>%
filter(!is.na(timepoints_models)) %>%
arrange(timepoint_cgGFAC_n) %>%
group_by(tumor_descriptor, cgGFAC, timepoint_cgGFAC_n, Kids_First_Biospecimen_ID, Variant_Classification) %>%
dplyr::count(timepoint_cgGFAC_n)
cgGFAC_id <- as.character(unique(df_plot_cgGFAC$cgGFAC))
cgGFAC_id <- sort(cgGFAC_id, decreasing = FALSE)
cgGFAC_id
[1] "ATRT" "DMG" "HGG" "LGG" "Other"
# Define parameters for function
x_value <- df_plot_cgGFAC$Kids_First_Biospecimen_ID
title <- paste("Variant types in PBTA cohort across cgGFAC", sep = " ")
# Run function
p <- create_stacked_barplot_variant_cgGFAC(count_df = df_plot_cgGFAC, x = x_value, palette = palette, title = title)

Alterations per timepoint in each cancer type and timepoint
model
tm_df_plot <- df_plot %>%
filter(!is.na(timepoints_models)) %>%
group_by(tumor_descriptor, cg_id, timepoints_models, Kids_First_Biospecimen_ID, Variant_Classification) %>%
dplyr::count(timepoint_cgGFAC_n)
tm <- as.character(unique(tm_df_plot$timepoints_models))
tm <- sort(tm, decreasing = FALSE)
tm
[1] "Dx-Dec" "Dx-Pro" "Dx-Pro-Dec" "Dx-Pro-Rec" "Dx-Pro-Rec-Dec" "Dx-Rec" "Dx-Rec-Dec" "Dx-SM"
[9] "Pro-Dec" "Pro-Rec" "Pro-Rec-Dec" "Rec-Dec" "Rec-SM"
# Loop through variable
for (i in seq_along(tm)){
print(i)
df_sub <- tm_df_plot %>%
filter(timepoints_models == tm[i])
# Define parameters for function
x_value <- df_sub$Kids_First_Biospecimen_ID
title <- paste(tm[i])
# Run function
p <- create_stacked_barplot_variant_cg_id(count_df = df_sub, x = x_value, palette = palette, title = title)
}
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sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.5.2
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggthemes_4.2.4 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
[9] tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 xfun_0.39 bslib_0.5.0 carData_3.0-5 colorspace_2.1-0 vctrs_0.6.3 generics_0.1.3
[8] htmltools_0.5.5 yaml_2.3.7 utf8_1.2.3 rlang_1.1.1 pillar_1.9.0 jquerylib_0.1.4 ggpubr_0.6.0
[15] glue_1.6.2 withr_2.5.0 bit64_4.0.5 lifecycle_1.0.3 munsell_0.5.0 ggsignif_0.6.4 gtable_0.3.3
[22] ragg_1.2.5 evaluate_0.21 labeling_0.4.2 knitr_1.43 tzdb_0.4.0 fastmap_1.1.1 parallel_4.2.3
[29] fansi_1.0.4 broom_1.0.5 scales_1.2.1 backports_1.4.1 cachem_1.0.8 vroom_1.6.3 jsonlite_1.8.7
[36] abind_1.4-5 systemfonts_1.0.4 farver_2.1.1 bit_4.0.5 textshaping_0.3.6 hms_1.1.3 digest_0.6.33
[43] stringi_1.7.12 rstatix_0.7.2 rprojroot_2.0.3 cli_3.6.1 tools_4.2.3 magrittr_2.0.3 sass_0.4.7
[50] crayon_1.5.2 car_3.1-2 pkgconfig_2.0.3 timechange_0.2.0 rmarkdown_2.23 rstudioapi_0.15.0 R6_2.5.1
[57] compiler_4.2.3
---
title: "Classification of Variants across paired longitudinal samples in the PBTA Cohort"
author: 'Antonia Chroni <chronia@chop.edu> for D3B'
date: "2023"
output:
  html_notebook:
    toc: TRUE
    toc_float: TRUE
---

# Set up
```{r load-library}
suppressPackageStartupMessages({
  library(tidyverse)
})
```

# Directories and File Inputs/Outputs
```{r set-dir-and-file-names}
# Detect the ".git" folder -- this will be in the project root directory
# Use this as the root directory to ensure proper sourcing of functions 
# no matter where this is called from
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
analysis_dir <- file.path(root_dir, "analyses", "tmb-vaf-longitudinal")
results_dir <- file.path(analysis_dir, "results")
input_dir <- file.path(analysis_dir, "input")
files_dir <- file.path(root_dir, "analyses", "sample-distribution-analysis", "results")

# Input files
pbta_file <- file.path(files_dir, "pbta.tsv") # file from add-sample-distribution module
genomic_paired_file <- file.path(files_dir, "genomic_assays_matched_time_points.tsv")
palette_file <- file.path(root_dir, "figures", "palettes", "oncoprint_color_palette.tsv")

# File path to plot directory
plots_dir <-
  file.path(analysis_dir, "plots")
if (!dir.exists(plots_dir)) {
  dir.create(plots_dir)
}

source(paste0(root_dir, "/figures/scripts/theme.R"))
source(paste0(analysis_dir, "/util/function-create-barplot.R"))
```

# Read in data and process

```{r load-process-inputs}
pbta_df <- readr::read_tsv(pbta_file, guess_max = 100000, show_col_types = FALSE) %>% 
  select(Kids_First_Participant_ID, Kids_First_Biospecimen_ID, cg_multiple, cg_id, cgGFAC, tumor_descriptor)

genomic_paired_df <- readr::read_tsv(genomic_paired_file, guess_max = 100000, show_col_types = FALSE) %>%
  left_join(pbta_df, by = c("Kids_First_Participant_ID")) 

descriptors_df <- genomic_paired_df %>%
  group_by(Kids_First_Participant_ID) %>%
  summarize(descriptors = paste(sort(tumor_descriptor), collapse = ", "),) 

# Vector to order timepoints
timepoints <- c("Diagnosis", "Progressive", "Recurrence", "Deceased", "Second Malignancy", "Unavailable")

# Create df to use for plots
df_plot <- genomic_paired_df %>% 
  left_join(descriptors_df, by = c("Kids_First_Participant_ID", "descriptors")) %>% 
  mutate(td_cgGFAC = case_when(grepl("Deceased", tumor_descriptor) ~ "xDeceased",
                               TRUE ~ tumor_descriptor),
         log10_tmb = abs(log10(tmb)),
         cg_id_kids = paste(cg_id, Kids_First_Participant_ID, sep = "_"),
         cg_id_kids = str_replace(cg_id_kids, "/", "_"),
         cg_id_kids = str_replace(cg_id_kids, "-", "_"),
         cg_id_kids = str_replace_all(cg_id_kids, " ", "_"),
         tumor_descriptor = factor(tumor_descriptor),
         tumor_descriptor = fct_relevel(tumor_descriptor, timepoints))

# Let's count number of samples 
count_df <- df_plot %>% 
  group_by(tumor_descriptor, cg_id, Kids_First_Biospecimen_ID, Variant_Classification) %>% 
  dplyr::count(cg_id) 

``` 

# Define parameters for plots

```{r define-parameters-for-plots}
# Read color palette
palette_df <- readr::read_tsv(palette_file, guess_max = 100000, show_col_types = FALSE) 

# Define and order palette
palette <- palette_df$hex_codes
names(palette) <- palette_df$color_names
```

# Alterations per timepoint

```{r plot-timepoint, fig.width = 6, fig.height = 6, fig.fullwidth = TRUE}
# Define parameters for function
x_value <- count_df$tumor_descriptor
title <- paste("Variant types in PBTA cohort", sep = " ")

# Run function
fname <- paste0(plots_dir, "/", "Alteration_type_timepoints_barplots.pdf")
print(fname)
p <- create_stacked_barplot_variant(count_df = count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 6, height = 6)
print(p)
dev.off()
```

# Alterations per timepoint in each cancer type

```{r plot-cg-id, fig.width = 30, fig.height = 18, fig.fullwidth = TRUE}
cg_id_id <- as.character(unique(count_df$cg_id)) 
cg_id_id <- sort(cg_id_id, decreasing = FALSE)
cg_id_id

# Define parameters for function
x_value <- count_df$Kids_First_Biospecimen_ID
title <- paste("Variant types in PBTA cohort across cancer groups", sep = " ")

# Run function
fname <- paste0(plots_dir, "/", "Alteration_type_timepoints_cg_id_barplots.pdf")
print(fname)
p <- create_stacked_barplot_variant_cg_id(count_df = count_df, x = x_value, palette = palette, title = title)
pdf(file = fname, width = 30, height = 18)
print(p)
dev.off()

```

# Alterations per timepoint in each cancer type defined by cgGFAC

```{r plot-cgGFAC-n-individual-plots, fig.width = 5, fig.height = 5, fig.fullwidth = TRUE}
df_plot_cgGFAC <- df_plot %>%
  filter(!is.na(timepoints_models)) %>% 
  arrange(timepoint_cgGFAC_n) %>% 
  group_by(tumor_descriptor, cgGFAC, timepoint_cgGFAC_n, Kids_First_Biospecimen_ID, Variant_Classification) %>% 
  dplyr::count(timepoint_cgGFAC_n)

cgGFAC_id <- as.character(unique(df_plot_cgGFAC$cgGFAC)) 
cgGFAC_id <- sort(cgGFAC_id, decreasing = FALSE)
cgGFAC_id

# Define parameters for function
x_value <- df_plot_cgGFAC$Kids_First_Biospecimen_ID
title <- paste("Variant types in PBTA cohort across cgGFAC", sep = " ")

# Run function
p <- create_stacked_barplot_variant_cgGFAC(count_df = df_plot_cgGFAC, x = x_value, palette = palette, title = title)

```

# Alterations per timepoint in each cancer type and timepoint model

```{r plot-timepoint-model, fig.width = 15, fig.height = 12, fig.fullwidth = TRUE}
tm_df_plot <- df_plot %>%
  filter(!is.na(timepoints_models)) %>% 
  group_by(tumor_descriptor, cg_id, timepoints_models, Kids_First_Biospecimen_ID, Variant_Classification) %>% 
  dplyr::count(timepoint_cgGFAC_n)

tm <- as.character(unique(tm_df_plot$timepoints_models))
tm <- sort(tm, decreasing = FALSE)
tm

# Loop through variable
for (i in seq_along(tm)){
  print(i)
  df_sub <- tm_df_plot %>%
      filter(timepoints_models == tm[i])
  
   # Define parameters for function
  x_value <- df_sub$Kids_First_Biospecimen_ID
  title <- paste(tm[i])
  
  # Run function
  p <- create_stacked_barplot_variant_cg_id(count_df = df_sub, x = x_value, palette = palette, title = title)
  
}
```


```{r echo=TRUE}
sessionInfo()
```
